Ensure VCF index exists for pbsv

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PbsvJointCallingHandler.java

@@ -176,7 +176,7 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
                     for (File f : outputs)
                     {
                         ctx.getFileManager().addIntermediateFile(f);
-                        ctx.getFileManager().addIntermediateFile(SequenceAnalysisService.get().ensureVcfIndex(f, ctx.getLogger(), true));
+                        ctx.getFileManager().addIntermediateFile(SequenceAnalysisService.get().ensureVcfIndex(f, ctx.getLogger(), false));
                     }
                     vcfOutGz = SequenceUtil.combineVcfs(outputs, genome, new File(ctx.getOutputDir(), outputBaseName + ".vcf.gz"), ctx.getLogger(), true, null, false);
                 }
@@ -361,6 +361,15 @@ public void verifyAndAddMissingSamples(JobContext ctx, File input, List<File> in
             sampleNamesInOrder.add(SequenceAnalysisService.get().getUnzippedBaseName(f.getName()));
         });
 
+        try
+        {
+            SequenceAnalysisService.get().ensureVcfIndex(input, ctx.getLogger(), false);
+        }
+        catch (IOException e)
+        {
+            throw new PipelineJobException(e);
+        }
+
         File output = new File(input.getPath() + ".tmp.vcf");
         try (VCFFileReader reader = new VCFFileReader(input))
         {

singlecell/resources/chunks/ClrNormalizeByGroup.R

@@ -1,8 +1,6 @@
 for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readRDS(seuratObjects[[datasetId]])
-    gc()
-
     seuratObj <- CellMembrane::ClrNormalizeByGroup(seuratObj, groupingVar = groupingVar, assayName = assayName, targetAssayName = targetAssayName, margin = margin, minCellsPerGroup = minCellsPerGroup, calculatePerFeatureUCell = calculatePerFeatureUCell, featureWhitelist = featureWhitelist, featureExclusionList = featureExclusionList)
 
     saveData(seuratObj, datasetId)